CI
b533a32bc8
Build pipeline: vsh-ci-template-7m7cc
Source commit: 73b07a96e0
Source message: Fix quotes in test (#4)
* Fix quotes in test
* query the first output file to pick up the 'name' value again and output it
grep with start and end position constaints
217 lines
7.5 KiB
JSON
217 lines
7.5 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "bgzip",
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"description": "Block compression/decompression utility",
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"type": "object",
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"definitions": {
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"inputs" : {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type":
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"string",
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"description": "Type: `file`, required. file to be compressed or decompressed",
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"help_text": "Type: `file`, required. file to be compressed or decompressed"
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}
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}
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},
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"outputs" : {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.output.output`. compressed or decompressed output",
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"help_text": "Type: `file`, required, default: `$id.$key.output.output`. compressed or decompressed output"
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,
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"default": "$id.$key.output.output"
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}
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,
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"index_name": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.index_name.index_name`. name of BGZF index file [file",
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"help_text": "Type: `file`, default: `$id.$key.index_name.index_name`. name of BGZF index file [file.gz.gzi]"
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,
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"default": "$id.$key.index_name.index_name"
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}
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}
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},
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"arguments" : {
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"title": "Arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"offset": {
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"type":
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"integer",
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"description": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)",
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"help_text": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)"
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}
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,
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"decompress": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. decompress the input file",
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"help_text": "Type: `boolean_true`, default: `false`. decompress the input file"
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,
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"default": "False"
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}
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,
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"rebgzip": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file",
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"help_text": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file"
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,
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"default": "False"
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}
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,
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"index": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. compress and create BGZF index",
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"help_text": "Type: `boolean_true`, default: `false`. compress and create BGZF index"
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,
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"default": "False"
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}
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,
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"compress_level": {
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"type":
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"integer",
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"description": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]",
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"help_text": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]"
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}
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,
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"reindex": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. (re)index the output file",
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"help_text": "Type: `boolean_true`, default: `false`. (re)index the output file"
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,
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"default": "False"
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}
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,
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"size": {
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"type":
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"integer",
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"description": "Type: `integer`. decompress INT bytes (uncompressed size)",
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"help_text": "Type: `integer`. decompress INT bytes (uncompressed size)"
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}
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,
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"test": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. test integrity of compressed file",
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"help_text": "Type: `boolean_true`, default: `false`. test integrity of compressed file"
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,
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"default": "False"
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}
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,
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"binary": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines",
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"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines"
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,
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"default": "False"
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}
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}
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},
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"nextflow input-output arguments" : {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
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"properties": {
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"publish_dir": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/inputs"
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},
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{
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"$ref": "#/definitions/outputs"
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},
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{
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"$ref": "#/definitions/arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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